Job ID = 11192651 sra ファイルのダウンロード中... Completed: 279K bytes transferred in 1 seconds (1560K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 7159 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924772/SRR3824803.sra Written 7159 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924772/SRR3824803.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:01 7159 reads; of these: 7159 (100.00%) were paired; of these: 2252 (31.46%) aligned concordantly 0 times 4593 (64.16%) aligned concordantly exactly 1 time 314 (4.39%) aligned concordantly >1 times ---- 2252 pairs aligned concordantly 0 times; of these: 211 (9.37%) aligned discordantly 1 time ---- 2041 pairs aligned 0 times concordantly or discordantly; of these: 4082 mates make up the pairs; of these: 2429 (59.51%) aligned 0 times 1517 (37.16%) aligned exactly 1 time 136 (3.33%) aligned >1 times 83.04% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1273 / 5072 = 0.2510 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 15 Sep 2018 09:41:50: # Command line: callpeak -t SRX1924772.bam -f BAM -g 12100000 -n SRX1924772.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924772.10 # format = BAM # ChIP-seq file = ['SRX1924772.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Sep 2018 09:41:50: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:41:50: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:41:50: # Command line: callpeak -t SRX1924772.bam -f BAM -g 12100000 -n SRX1924772.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924772.05 # format = BAM # ChIP-seq file = ['SRX1924772.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Sep 2018 09:41:50: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:41:50: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:41:50: # Command line: callpeak -t SRX1924772.bam -f BAM -g 12100000 -n SRX1924772.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924772.20 # format = BAM # ChIP-seq file = ['SRX1924772.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Sep 2018 09:41:50: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:41:50: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Sep 2018 09:41:50: #1 tag size is determined as 39 bps INFO @ Sat, 15 Sep 2018 09:41:50: #1 tag size = 39 INFO @ Sat, 15 Sep 2018 09:41:50: #1 total tags in treatment: 3654 INFO @ Sat, 15 Sep 2018 09:41:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:41:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:41:50: #1 tag size is determined as 39 bps INFO @ Sat, 15 Sep 2018 09:41:50: #1 tag size = 39 INFO @ Sat, 15 Sep 2018 09:41:50: #1 total tags in treatment: 3654 INFO @ Sat, 15 Sep 2018 09:41:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:41:50: #1 tag size is determined as 39 bps INFO @ Sat, 15 Sep 2018 09:41:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:41:50: #1 tag size = 39 INFO @ Sat, 15 Sep 2018 09:41:50: #1 total tags in treatment: 3654 INFO @ Sat, 15 Sep 2018 09:41:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:41:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:41:50: #1 tags after filtering in treatment: 3652 INFO @ Sat, 15 Sep 2018 09:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:41:50: #1 finished! INFO @ Sat, 15 Sep 2018 09:41:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:41:50: #1 tags after filtering in treatment: 3652 INFO @ Sat, 15 Sep 2018 09:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:41:50: #1 finished! INFO @ Sat, 15 Sep 2018 09:41:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:41:50: #1 tags after filtering in treatment: 3652 INFO @ Sat, 15 Sep 2018 09:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:41:50: #1 finished! INFO @ Sat, 15 Sep 2018 09:41:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:41:50: #2 number of paired peaks: 161 WARNING @ Sat, 15 Sep 2018 09:41:50: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Sep 2018 09:41:50: start model_add_line... INFO @ Sat, 15 Sep 2018 09:41:50: #2 number of paired peaks: 161 WARNING @ Sat, 15 Sep 2018 09:41:50: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Sep 2018 09:41:50: start X-correlation... INFO @ Sat, 15 Sep 2018 09:41:50: start model_add_line... INFO @ Sat, 15 Sep 2018 09:41:50: #2 number of paired peaks: 161 INFO @ Sat, 15 Sep 2018 09:41:50: start X-correlation... WARNING @ Sat, 15 Sep 2018 09:41:50: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Sep 2018 09:41:50: start model_add_line... INFO @ Sat, 15 Sep 2018 09:41:50: start X-correlation... BigWig に変換しました。 INFO @ Sat, 15 Sep 2018 09:41:50: end of X-cor INFO @ Sat, 15 Sep 2018 09:41:50: end of X-cor INFO @ Sat, 15 Sep 2018 09:41:50: end of X-cor INFO @ Sat, 15 Sep 2018 09:41:50: #2 finished! INFO @ Sat, 15 Sep 2018 09:41:50: #2 finished! INFO @ Sat, 15 Sep 2018 09:41:50: #2 finished! INFO @ Sat, 15 Sep 2018 09:41:50: #2 predicted fragment length is 288 bps INFO @ Sat, 15 Sep 2018 09:41:50: #2 predicted fragment length is 288 bps INFO @ Sat, 15 Sep 2018 09:41:50: #2 predicted fragment length is 288 bps INFO @ Sat, 15 Sep 2018 09:41:50: #2 alternative fragment length(s) may be 9,82,119,175,192,225,288,359,390,501,563 bps INFO @ Sat, 15 Sep 2018 09:41:50: #2 alternative fragment length(s) may be 9,82,119,175,192,225,288,359,390,501,563 bps INFO @ Sat, 15 Sep 2018 09:41:50: #2 alternative fragment length(s) may be 9,82,119,175,192,225,288,359,390,501,563 bps INFO @ Sat, 15 Sep 2018 09:41:50: #2.2 Generate R script for model : SRX1924772.10_model.r INFO @ Sat, 15 Sep 2018 09:41:50: #2.2 Generate R script for model : SRX1924772.05_model.r INFO @ Sat, 15 Sep 2018 09:41:50: #2.2 Generate R script for model : SRX1924772.20_model.r INFO @ Sat, 15 Sep 2018 09:41:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:41:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:41:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:41:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:41:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:41:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:41:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:41:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:41:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:41:50: #4 Write output xls file... SRX1924772.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:41:50: #4 Write output xls file... SRX1924772.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:41:50: #4 Write output xls file... SRX1924772.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:41:50: #4 Write peak in narrowPeak format file... SRX1924772.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:41:50: #4 Write peak in narrowPeak format file... SRX1924772.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:41:50: #4 Write peak in narrowPeak format file... SRX1924772.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:41:50: #4 Write summits bed file... SRX1924772.10_summits.bed INFO @ Sat, 15 Sep 2018 09:41:50: #4 Write summits bed file... SRX1924772.05_summits.bed INFO @ Sat, 15 Sep 2018 09:41:50: #4 Write summits bed file... SRX1924772.20_summits.bed INFO @ Sat, 15 Sep 2018 09:41:50: Done! INFO @ Sat, 15 Sep 2018 09:41:50: Done! INFO @ Sat, 15 Sep 2018 09:41:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling